Few studies on human papillomavirus (HPV) have been conducted in Mongolia. This study was performed to evaluate the prevalent HPV genotypes and their associations with cytology and demographic and behavioral characteristics in Mongolian women with cervical abnormalities. Methods: Exfoliated cell samples of 100 women who had a previous history of cervical abnormality were collected. Cytological interpretation was conducted microscopically and HPV genotyping was performed using the Roche Linear Array test. Study questionnaires were completed. Results: Overall, 25 HPV genotypes were detected in 47% of participants, and the most prevalent were HPV 16, 52, 58, and 33. Cytological examination revealed 12% of participants had atypical squamous cells of undetermined significance (ASC-US), 8% had low-grade squamous intraepithelial lesions (LSIL), 7% had high-grade squamous intraepithelial lesions (HSIL), and 14% had squamous cell carcinoma (SCC), while 59% of women had a normal cytology. HPV 16 was the most common type among women with a normal cytology and cervical cancer. However, women with cervical abnormalities including LSIL and HSIL were predominantly infected with HPV 52. Moreover, women aged <35 years had a significantly higher risk of HPV infection than those in the other age groups (p < 0.05). Conclusions: The prevalent trend of HPV genotypes observed in this cohort differs from that reported previously in Mongolia. These data may contribute to developing an effective strategy for cervical cancer prevention in Mongolia.